snpMatrix-package |
The snp.matrix and X.snp.matrix classes |
Asnps |
Test data for the snpMatrix package |
Autosomes |
Test data for the snpMatrix package |
cbind |
Bind together two or more snp.matrix objects |
cbind,snp.matrix-method |
Class "snp.matrix" |
cbind2 |
Bind together two or more snp.matrix objects |
cbind2,snp.matrix,snp.matrix-method |
Class "snp.matrix" |
coerce,matrix,snp.matrix-method |
Class "snp.matrix" |
coerce,snp,character-method |
Class "snp" |
coerce,snp,genotype-method |
Class "snp" |
coerce,snp,numeric-method |
Class "snp" |
coerce,snp.matrix,character-method |
Class "snp.matrix" |
coerce,snp.matrix,numeric-method |
Class "snp.matrix" |
coerce,snp.matrix,X.snp.matrix-method |
Class "X.snp.matrix" |
coerce,X.snp,character-method |
Class "X.snp" |
coerce,X.snp,genotype-method |
Class "X.snp" |
coerce,X.snp,numeric-method |
Class "X.snp" |
coerce,X.snp.matrix,character-method |
Class "X.snp.matrix" |
epsout.ld.snp |
Function to write an eps file directly to visualize LD |
for.exercise |
Data for exercise in use of the snpMatrix package |
genotype-class |
snpMatrix-internal |
glm.test.control |
Set up control object for GLM tests |
haplotype-class |
snpMatrix-internal |
ibs.stats |
function to calculate the identity-by-state stats of a group of samples |
ibsCount |
Count alleles identical by state |
ibsDist |
Distance matrix based on identity by state (IBS) |
initialize,snp.matrix-method |
Class "snp.matrix" |
initialize,X.snp.matrix-method |
Class "X.snp.matrix" |
is.na,snp.matrix-method |
Class "snp.matrix" |
ld.snp |
Function to calculate pairwise D', $r^2$ |
ld.with |
function to calculate the LD measures of specific SNPs against other SNPs |
ld.with,snp.matrix,character-method |
function to calculate the LD measures of specific SNPs against other SNPs |
niceprint |
Class "snp.dprime" for Results of LD calculation |
pair.result.ld.snp |
Function to calculate the pairwise D', $r^2$, LOD of a pair of specified SNPs |
plot.snp.dprime |
Function to draw the pairwise D' in a eps file |
print.snp.dprime |
Class "snp.dprime" for Results of LD calculation |
qq.chisq |
Quantile-quantile plot for chi-squared tests |
rbind |
Bind together two or more snp.matrix objects |
rbind,snp.matrix-method |
Class "snp.matrix" |
rbind2 |
Bind together two or more snp.matrix objects |
rbind2,snp.matrix,snp.matrix-method |
Class "snp.matrix" |
read.HapMap.data |
function to import HapMap genotype data as snp.matrix |
read.pedfile.info |
function to read the accompanying info file of a LINKAGE ped file |
read.snps.chiamo |
Read genotype data from the output of Chiamo |
read.snps.long |
Read SNP data in long format |
read.snps.long.old |
Read SNP input data in "long" format (old version) |
read.snps.pedfile |
Read genotype data from a LINKAGE "pedfile" |
read.wtccc.signals |
read normalized signals in the WTCCC signal file format |
row.summary |
Summarize rows of a snp matrix |
show,snp-method |
Class "snp" |
show,snp.matrix-method |
Class "snp.matrix" |
show,X.snp-method |
Class "X.snp" |
show,X.snp.matrix-method |
Class "X.snp.matrix" |
single.snp.tests |
1-df and 2-df tests for genetic associations with SNPs |
snp-class |
Class "snp" |
snp.cbind |
Bind together two or more snp.matrix objects |
snp.cor |
Correlations with columns of a snp.matrix |
snp.dprime-class |
Class "snp.dprime" for Results of LD calculation |
snp.lhs.tests |
Score tests with SNP genotypes as dependent variable |
snp.matrix-class |
Class "snp.matrix" |
snp.post |
Pre- or post-multiply a snp.matrix object by a general matrix |
snp.pre |
Pre- or post-multiply a snp.matrix object by a general matrix |
snp.rbind |
Bind together two or more snp.matrix objects |
snp.rhs.tests |
Score tests with SNP genotypes as independent variable |
snp.support |
Data for exercise in use of the snpMatrix package |
snpMatrix |
The snp.matrix and X.snp.matrix classes |
snps.10 |
Data for exercise in use of the snpMatrix package |
subject.data |
Test data for the snpMatrix package |
subject.support |
Data for exercise in use of the snpMatrix package |
summary,snp.matrix-method |
Class "snp.matrix" |
summary,X.snp.matrix-method |
Class "X.snp.matrix" |
testdata |
Test data for the snpMatrix package |
write.snp.matrix |
Write a snp.matrix object as a text file |
wtccc.sample.list |
read the sample list from the header of the WTCCC signal file format |
X.snp-class |
Class "X.snp" |
X.snp.matrix-class |
Class "X.snp.matrix" |
Xchromosome |
Test data for the snpMatrix package |
Xsnps |
Test data for the snpMatrix package |
xxt |
X.X-transpose for a normalised snp.matrix |
[,snp.matrix-method |
Class "snp.matrix" |
[,X.snp.matrix-method |
Class "X.snp.matrix" |
[<-,X.snp.matrix,ANY,ANY,X.snp.matrix-method |
Class "X.snp.matrix" |